RetrogeneDB ID:

retro_pabe_3474

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:9:55196148..55196681(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PPIA
Ensembl ID:ENSPPYG00000017586
Aliases:None
Description:peptidyl-prolyl cis-trans isomerase A [Source:RefSeq peptide;Acc:NP_001126060]


Retrocopy-Parental alignment summary:






>retro_pabe_3474
TTTGCAGATGCCTTTGCCATCGGGTGCCCTGTACTGTCAGCCATCATCAACCCCACCATGTTCTTCAACGTCGCCGTGGA
TGGTGGGCCCTTGGGCTGCGTCTCCTTCGAGCTGTTTGCAGACAAGTTTCCAAAGACAGCAGGAAACTTTCATGCTCTGA
GCACTGGAGAGAAAGGATTTGGTTATAAGGGTTCCTGCTTTCACAGAATTATTCCAGGGTTTATGTGTCAGGGTGGTGAA
TTCACACATCATAATGGCACTGACAGCAAGTCAATCTATGGGGAGAAATTTGATGATGAGAACTTCATCCTAAAGCATAC
AGGTCCTGGCATCTTGTCCATGGCAAATGCTGAACCCAACACAAACGGTTCCCAGTTTTGCATCTGCACTGCCAAGACTG
AGTGGTTGGATGGCAAGCATGTGGTCTTTGGCAAGGTGAAAGAAGGCATGAATTTTGTGGAGGCCATGGAGCGCTTTGGT
TCAGGAATGGCAAGACCAGCAAGAAGATCAGCATTACTGACTGTGGGCAACTC

ORF - retro_pabe_3474 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.78 %
Parental protein coverage: 58.5 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalFADAAAEENRVLLAMVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRI
FADA.A....VL.A..NPT.FF..AVDG.PLG.VSFELFADK.PKTA.NF.ALSTGEKGFGYKGSCFHRI
RetrocopyFADAFAIGCPVLSAIINPTMFFNVAVDGGPLGCVSFELFADKFPKTAGNFHALSTGEKGFGYKGSCFHRI
ParentalIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKH
IPGFMCQGG.FT.HNGT..KSIYGEKF.DENFILKHTGPGILSMANA.PNTNGSQF.ICTAKTEWLDGKH
RetrocopyIPGFMCQGGEFTHHNGTDSKSIYGEKFDDENFILKHTGPGILSMANAEPNTNGSQFCICTAKTEWLDGKH
ParentalVPLMSKVKEGMNIVEAMERFGS-RNGKTSKKITIADCGQL
V....KVKEGMN.VEAMERFGS.RNGKTSKKI.I.DCGQL
RetrocopyV-VFGKVKEGMNFVEAMERFGS<RNGKTSKKISITDCGQL

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP007412_brain_prefrontal_cortex 0 .00 RPM 59 .44 RPM
SRP007412_cerebellum 0 .00 RPM 20 .06 RPM
SRP007412_heart 0 .06 RPM 9 .57 RPM
SRP007412_kidney 0 .03 RPM 39 .21 RPM
SRP007412_liver 0 .00 RPM 21 .57 RPM
Pongo abelii was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_pabe_3474 retrocopy.
Pongo abelii was not studied using FANTOM5 data.
retro_pabe_3474 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_3474 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_4128
Pan troglodytes retro_ptro_2806

Parental genes homology:
Parental genes homology involve 21 parental genes, and 464 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG0000001200312 retrocopies
Callithrix jacchus ENSCJAG0000001196954 retrocopies
Cavia porcellus ENSCPOG0000000263211 retrocopies
Echinops telfairi ENSETEG0000000218621 retrocopies
Homo sapiens ENSG0000019626278 retrocopies
Gorilla gorilla ENSGGOG000000262984 retrocopies
Loxodonta africana ENSLAFG000000113451 retrocopy
Macropus eugenii ENSMEUG0000000201620 retrocopies
Macaca mulatta ENSMMUG0000001663810 retrocopies
Monodelphis domestica ENSMODG000000160899 retrocopies
Mus musculus ENSMUSG000000718662 retrocopies
Oryctolagus cuniculus ENSOCUG000000166623 retrocopies
Otolemur garnettii ENSOGAG0000002799731 retrocopies
Pongo abelii ENSPPYG00000017586 12 retrocopies
Pongo abelii ENSPPYG000000175874 retrocopies
Pan troglodytes ENSPTRG0000002306477 retrocopies
Rattus norvegicus ENSRNOG000000064232 retrocopies
Sarcophilus harrisii ENSSHAG000000170623 retrocopies
Ictidomys tridecemlineatus ENSSTOG0000001021510 retrocopies
Tupaia belangeri ENSTBEG0000001748477 retrocopies
Tarsius syrichta ENSTSYG0000000897323 retrocopies



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